/*
 * RepeatAnalyserMain.cc
 *
 *  Created on: Apr 18, 2013
 *      Author: hxin
 */

#include "RepeatAnalyser.h"
#include <cstdlib>

int main(int argc, char * argv[]) {
	RepeatAnalyser Analyser;
	if (argc == 4) {
		string refName = argv[1];
		string hashName = argv[2];
		int chromoNum = atoi(argv[3]);

		cout << "Loading" << endl;
		//Analyser.loadHashFile(hashName);
		Analyser.loadRefFile(refName);
		Analyser.loadHashFile(hashName);
		Analyser.loadChromo(chromoNum);
		Analyser.markRepeat(1);
		//Analyser.markTandemRepeat(0);
	}
	else {
		cerr << "Usage: $> ./RepeatAnalyser refName hashName chromoNum" << endl;
	}

}

